Genome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retrieved in a single study contributed by the cost-effective short-read sequencing and developed assembly/binning pipelines. However, conventional binning methods usually yield highly fragmented draft genomes that limit our ability to comprehensively understand these microbial communities. Thus, to leverage advantage of both the long and short reads to retrieve more complete genomes from environmental samples is a must-do task to move this direction forward. Here, we used an iterative hybrid assembly (IHA) approach to reconstruct 49 metagenome-assembled genomes (MAGs), including 27 high-quality (HQ) and high-contiguity (HC) genomes with contig number ≤ 5, eight of which were circular finished genomes from a partial-nitritation anammox (PNA) reactor. These 49 recovered MAGs (43 MAGs encoding full-length rRNA, average N50 of 2.2 Mbp), represented the majority (92.3%) of the bacterial community. Moreover, the workflow retrieved HQ and HC MAGs even with an extremely low coverage (relative abundance < 0.1%). Among them, 34 MAGs could not be assigned to the genus level, indicating the novelty of the genomes retrieved using the IHA method proposed in this study. Comparative analysis of HQ MAG pairs reconstructed using two methods, i.e., hybrid and short reads only, revealed that identical genes in the MAG pairs represented 87.5% and 95.5% of the total gene inventory of hybrid and short reads only assembled MAGs, respectively. In addition, the first finished anammox genome of the genus Ca. Brocadia reconstructed revealed that there were two identical hydrazine synthase (hzs) genes, providing the exact gene copy number of this crucial phylomarker of anammox at the genome level. Our results showcased the high-quality and high-contiguity genome retrieval performance and demonstrated the feasibility of complete genome reconstruction using the IHA workflow from the enrichment system. These (near-) complete genomes provided a high resolution of the microbial community, which might help to understand the bacterial repertoire of anammox-associated systems. Combined with other validation experiments, the workflow can enable a detailed view of the anammox or other similar enrichment systems.

中文翻译：

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通过迭代混合组装方法获得部分亚硝化/厌氧氨氧化系统的高质量细菌基因组


以基因组为中心的方法广泛用于研究各种环境系统内的微生物组成、动力学、生态和相互作用。通过具有成本效益的短读长测序和开发的组装/装箱管道，可以在一项研究中检索数百甚至数千个基因组。然而，传统的分箱方法通常会产生高度碎片化的基因组草案，这限制了我们全面了解这些微生物群落的能力。因此，利用长读和短读的优势从环境样本中检索更完整的基因组是推动这一方向前进的必须要做的任务。在这里，我们使用迭代混合组装（IHA）方法重建了49个宏基因组组装基因组（MAG），其中包括27个重叠群数≤5的高质量（HQ）和高连续性（HC）基因组，其中8个是环状的来自部分亚硝化厌氧氨氧化（PNA）反应器的成品基因组。这 49 个回收的 MAG（43 个 MAG 编码全长 rRNA，平均 N50 为 2.2 Mbp）代表了细菌群落的大多数（92.3%）。此外，即使覆盖率极低（相对丰度 < 0.1%），该工作流程也能检索到 HQ 和 HC MAG。其中，34个MAG无法归属到属水平，表明使用本研究提出的IHA方法检索的基因组的新颖性。使用混合和仅短读两种方法重建的 HQ MAG 对的比较分析表明，MAG 对中的相同基因分别占混合和仅短读组装 MAG 总基因库存的 87.5% 和 95.5%。此外，第一个完成的Ca属厌氧氨氧化基因组。 Brocadia 重建揭示了存在两个相同的肼合酶 (hzs) 基因，在基因组水平上提供了厌氧氨氧化这一重要系统标记的准确基因拷贝数。我们的结果展示了高质量和高连续性的基因组检索性能，并证明了使用富集系统的 IHA 工作流程进行完整基因组重建的可行性。这些（接近）完整的基因组提供了微生物群落的高分辨率，这可能有助于了解厌氧氨氧化相关系统的细菌库。与其他验证实验相结合，该工作流程可以实现厌氧氨氧化或其他类似富集系统的详细视图。